Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

27902974 .. 27907580

Gene Structure 4607 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG133100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 336 bp

ATGGTTCTCACGACTAAACTTTGCCGCTTCAGTGGTGCCAAGATCTACCCTGGTAGGGGCATCAGATTCATCCACTCCGATTCTCAGCATGCTTACAACCCAAATGAGGAGTATGCAGATGTGGAATCCACATTGCGTTCGCATTTGGAATCTTTTCTAGAAACTACAAGATCATTCAATATGATTTACACCAAGTTGTGTAAAAGGGACATACTCTTATCTACTACCTTGAAATGTCGTGCTTTTGCAGGAAATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCTGCAGCCAATCGCTTAGTGGAGGCATATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005819 GO:0005856 GO:0005874 GO:0005876 GO:0008017 GO:0008092 GO:0009524 GO:0015630 GO:0015631 GO:0043226 GO:0043228 GO:0043229 GO:0043232 GO:0044422 GO:0044424 GO:0044430 GO:0044444 GO:0044446 GO:0044464 GO:0051011 GO:0099080 GO:0099081 GO:0099512 GO:0099513

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Plant_NMP1

Protein Analysis

111

Amino Acids

12.36

Weight (kDa)

8.78

Isoelectric Point (pI)

41.23

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ribosomal_L24e	PF01246	5 - 29	1.2e-07	Ribosomal protein L24e
Plant_NMP1	PF06694	28 - 66	2.2e-13	Plant nuclear matrix protein 1 (NMP1)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000643)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G28230
fragaria_vesca	FvH4_3g16300 FvH4_6g12751 FvH4_6g44570 FvH4_6g44594 FvH4_7g07660
malus_domestica	MD09G1096400.v1.1 MD17G1084500.v1.1
prunus_persica	Prupe.3G231100_v2.0.a1
pyrus_communis	pycom09g02090 pycom17g08160
rosa_chinensis	RchiOBHm_Chr1g0342751 RchiOBHm_Chr2g0157591 RchiOBHm_Chr2g0161781 RchiOBHm_Chr3g0469881
rosa_laevigata	RLG00000007135 RLG00000010298 RLG00000021299 RLG00000021302 RLG00000029173 RLG00000029192
rosa_multiflora	Rmu_sc0000173.1_g000045 Rmu_sc0001403.1_g000033 Rmu_sc0001403.1_g000034 Rmu_sc0001993.1_g000002 Rmu_sc0001993.1_g000020 Rmu_sc0003662.1_g000014 Rmu_sc0011563.1_g000010 Rmu_sc0012276.1_g000010 Rmu_sc0026352.1_g000003
rosa_roxburghii	Rroxscaffold_1G00038970 Rroxscaffold_2G00088610 Rroxscaffold_3G00231870 Rroxscaffold_4G00288710 Rroxscaffold_4G00313230 Rroxscaffold_6G00396080 Rroxscaffold_7G00184860
rosa_rugosa	Rorug01G0146100.1 Rorug02G0491800 Rorug02G0492600 Rorug03G0291200 Rorug05G0303900 Rorug05G0335100 Rorug05G0335200
rosa_samantha	Rh1AG028300 Rh1AG137400 Rh1AG162800 Rh1AG163600 Rh1AG163700 Rh1AG164400 Rh1AG164500 Rh1BG129500 Rh1BG129600 Rh1CG025800 Rh1CG129600 Rh1CG151800 Rh1CG152300 Rh1CG152800 Rh1CG153300 Rh1DG044700 Rh1DG133100 Rh2AG558000 Rh2BG571600 Rh2CG541700 Rh2DG549600 Rh2DG580500 Rh3BG178200 Rh3CG168900 Rh3DG076100 Rh3DG260000 Rh5AG515900 Rh6BG166400 Rh6DG108300 Rh7AG194200 Rh7DG200800 Rh7DG369800
rosa_wichuraiana	Rw2G046170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	281
AccB1I	GGYRCC	2 cut(s)	35, 281
AciI	CCGC	1 cut(s)	25
AcuI	CTGAAG	1 cut(s)	13
AfaI	GTAC	1 cut(s)	283
AfiI	CCNNNNNNNGG	3 cut(s)	55, 56, 106
AgsI	TTSAA	2 cut(s)	178, 232
AjnI	CCWGG	2 cut(s)	49, 261
AluBI	AGCT	1 cut(s)	290
AluI	AGCT	1 cut(s)	290
AoxI	GGCC	1 cut(s)	303
ApeKI	GCWGC	1 cut(s)	309
Asp700I	GAANNNNTTC	1 cut(s)	153
Asp718I	GGTACC	1 cut(s)	281
AspS9I	GGNCC	1 cut(s)	303
BanI	GGYRCC	2 cut(s)	35, 281
BbvI	GCAGC	1 cut(s)	321
BccI	CCATC	1 cut(s)	269
BciT130I	CCWGG	2 cut(s)	51, 263
BfaI	CTAG	1 cut(s)	158
BfmI	CTRYAG	1 cut(s)	307
BglII	AGATCT	1 cut(s)	42
BisI	GCNGC	2 cut(s)	25, 310
BlsI	GCNGC	2 cut(s)	26, 311
Bme1390I	CCNGG	2 cut(s)	51, 263
BmgT120I	GGNCC	1 cut(s)	303
BmiI	GGNNCC	2 cut(s)	37, 283
BmrFI	CCNGG	2 cut(s)	51, 263
BmsI	GCATC	1 cut(s)	69
BsaJI	CCNNGG	3 cut(s)	49, 261, 293
BsaXI	ACNNNNNCTCC	2 cut(s)	274, 304
Bsc4I	CCNNNNNNNGG	3 cut(s)	55, 56, 106
Bse3DI	GCAATG	1 cut(s)	131
BseBI	CCWGG	2 cut(s)	51, 263
BseDI	CCNNGG	3 cut(s)	49, 261, 293
BseGI	GGATG	1 cut(s)	69
BseLI	CCNNNNNNNGG	3 cut(s)	55, 56, 106
BseMI	GCAATG	1 cut(s)	131
BseMII	CTCAG	1 cut(s)	98
BseRI	GAGGAG	1 cut(s)	122
BseXI	GCAGC	1 cut(s)	321
BseYI	CCCAGC	1 cut(s)	286
BshFI	GGCC	1 cut(s)	305
BshNI	GGYRCC	2 cut(s)	35, 281
BslFI	GGGAC	2 cut(s)	221, 244
BslI	CCNNNNNNNGG	3 cut(s)	55, 56, 106
BsmFI	GGGAC	2 cut(s)	221, 244
BsnI	GGCC	1 cut(s)	305
Bsp143I	GATC	2 cut(s)	42, 170
Bsp19I	CCATGG	1 cut(s)	293
BspACI	CCGC	1 cut(s)	25
BspANI	GGCC	1 cut(s)	305
BspCNI	CTCAG	1 cut(s)	97
BspLI	GGNNCC	2 cut(s)	37, 283
BspMAI	CTGCAG	1 cut(s)	311
BspT107I	GGYRCC	2 cut(s)	35, 281
BsrDI	GCAATG	1 cut(s)	131
BssECI	CCNNGG	3 cut(s)	49, 261, 293
BssMI	GATC	2 cut(s)	42, 170
BssT1I	CCWWGG	1 cut(s)	293
Bst2UI	CCWGG	2 cut(s)	51, 263
BstC8I	GCNNGC	2 cut(s)	90, 307
BstDEI	CTNAG	2 cut(s)	84, 320
BstDSI	CCRYGG	1 cut(s)	293
BstF5I	GGATG	1 cut(s)	69
BstKTI	GATC	2 cut(s)	45, 173
BstMBI	GATC	2 cut(s)	42, 170
BstNI	CCWGG	2 cut(s)	51, 263
BstNSI	RCATGY	1 cut(s)	92
BstSCI	CCNGG	2 cut(s)	49, 261
BstSFI	CTRYAG	1 cut(s)	307
BstV1I	GCAGC	1 cut(s)	321
BstX2I	RGATCY	1 cut(s)	42
BstXI	CCANNNNNNTGG	1 cut(s)	294
BstYI	RGATCY	1 cut(s)	42
BsuRI	GGCC	1 cut(s)	305
BtgI	CCRYGG	1 cut(s)	293
BtsCI	GGATG	1 cut(s)	69
BtsIMutI	CAGTG	1 cut(s)	37
Cac8I	GCNNGC	2 cut(s)	90, 307
Cfr13I	GGNCC	1 cut(s)	303
Csp6I	GTAC	1 cut(s)	282
CviAII	CATG	3 cut(s)	89, 272, 294
CviJI	RGCY	3 cut(s)	290, 305, 312
CviKI_1	RGCY	3 cut(s)	290, 305, 312
CviQI	GTAC	1 cut(s)	282
DdeI	CTNAG	2 cut(s)	84, 320
DpnI	GATC	2 cut(s)	44, 172
DpnII	GATC	2 cut(s)	42, 170
Eco130I	CCWWGG	1 cut(s)	293
Eco57I	CTGAAG	1 cut(s)	13
EcoRII	CCWGG	2 cut(s)	49, 261
EcoT14I	CCWWGG	1 cut(s)	293
ErhI	CCWWGG	1 cut(s)	293
FaeI	CATG	3 cut(s)	92, 275, 297
FaiI	YATR	8 cut(s)	90, 114, 182, 212, 273, 295, 332, 334
FaqI	GGGAC	2 cut(s)	221, 244
FatI	CATG	3 cut(s)	88, 271, 293
Fnu4HI	GCNGC	2 cut(s)	25, 310
FokI	GGATG	1 cut(s)	56
Fsp4HI	GCNGC	2 cut(s)	25, 310
FspBI	CTAG	1 cut(s)	158
GluI	GCNGC	2 cut(s)	25, 310
GsaI	CCCAGC	1 cut(s)	290
HaeIII	GGCC	1 cut(s)	305
Hin1II	CATG	3 cut(s)	92, 275, 297
HinfI	GANTC	4 cut(s)	66, 80, 125, 149
Hpy188I	TCNGA	2 cut(s)	65, 79
Hpy188III	TCNNGA	2 cut(s)	10, 158
HpyCH4IV	ACGT	1 cut(s)	257
HpyCH4V	TGCA	3 cut(s)	116, 248, 309
HpyF3I	CTNAG	2 cut(s)	84, 320
HpySE526I	ACGT	1 cut(s)	257
Hsp92II	CATG	3 cut(s)	92, 275, 297
KpnI	GGTACC	1 cut(s)	285
Kzo9I	GATC	2 cut(s)	42, 170
LmnI	GCTCC	1 cut(s)	295
LpnPI	CCDG	7 cut(s)	36, 63, 234, 248, 275, 300, 319
Lsp1109I	GCAGC	1 cut(s)	321
LweI	GCATC	1 cut(s)	69
MaeI	CTAG	1 cut(s)	158
MaeII	ACGT	1 cut(s)	257
MalI	GATC	2 cut(s)	44, 172
MboI	GATC	2 cut(s)	42, 170
MflI	RGATCY	1 cut(s)	42
MnlI	CCTC	3 cut(s)	100, 272, 320
MroXI	GAANNNNTTC	1 cut(s)	153
MspR9I	CCNGG	2 cut(s)	51, 263
MvaI	CCWGG	2 cut(s)	51, 263
NcoI	CCATGG	1 cut(s)	293
NdeII	GATC	2 cut(s)	42, 170
NlaIII	CATG	3 cut(s)	92, 275, 297
NlaIV	GGNNCC	2 cut(s)	37, 283
NspI	RCATGY	1 cut(s)	92
PaeI	GCATGC	1 cut(s)	92
PdmI	GAANNNNTTC	1 cut(s)	153
PfeI	GAWTC	4 cut(s)	66, 80, 125, 149
PkrI	GCNGC	2 cut(s)	26, 311
Psp6I	CCWGG	2 cut(s)	49, 261
PspFI	CCCAGC	1 cut(s)	286
PspGI	CCWGG	2 cut(s)	49, 261
PspN4I	GGNNCC	2 cut(s)	37, 283
PspPI	GGNCC	1 cut(s)	303
PstI	CTGCAG	1 cut(s)	311
PsuI	RGATCY	1 cut(s)	42
RsaI	GTAC	1 cut(s)	283
RsaNI	GTAC	1 cut(s)	282
SatI	GCNGC	2 cut(s)	25, 310
Sau3AI	GATC	2 cut(s)	42, 170
Sau96I	GGNCC	1 cut(s)	303
ScrFI	CCNGG	2 cut(s)	51, 263
SetI	ASST	4 cut(s)	230, 260, 283, 292
SfaNI	GCATC	1 cut(s)	69
SfcI	CTRYAG	1 cut(s)	307
SphI	GCATGC	1 cut(s)	92
SsiI	CCGC	1 cut(s)	25
SspMI	CTAG	1 cut(s)	158
StyD4I	CCNGG	2 cut(s)	49, 261
StyI	CCWWGG	1 cut(s)	293
TaiI	ACGT	1 cut(s)	260
TauI	GCSGC	1 cut(s)	27
TfiI	GAWTC	4 cut(s)	66, 80, 125, 149
TscAI	CASTG	1 cut(s)	37
TseI	GCWGC	1 cut(s)	309
TspDTI	ATGAA	1 cut(s)	58
TspRI	CASTG	1 cut(s)	37
XbaI	TCTAGA	1 cut(s)	157
XceI	RCATGY	1 cut(s)	92
XcmI	CCANNNNNNNNNTGG	1 cut(s)	320
XmnI	GAANNNNTTC	1 cut(s)	153
XspI	CTAG	1 cut(s)	158

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.